Scientists at the National Institute of Science Education and Research (NISER), Bhubaneswar, have uncovered the molecular mechanism behind Gram-negative bacteria’s resistance to the drug PC190723, revealing how intra-molecular interactions in proteins, such as salt bridges, prevent the drug from binding effectively.
Antibiotic resistance (AMR) has become one of the world’s most pressing health concerns, according to the World Health Organization (WHO). While antibiotics have revolutionised medicine by treating countless diseases, their misuse and overuse, especially in the late 20th century, have led to widespread resistance and the emergence of multi-drug resistant strains. With the advent of technology, antibiotic research has made significant strides, leading to the development of new drugs by scientists targeting proteins essential for cell survival.
Ramanujam Srinivasan, Associate Professor, National Institute of Science, Education and Research (NISER), Bhubaneshwar, and co-author of the study, highlights the importance of this approach in scientific research. In a recent study, Srinivasan in collaboration with Gayathri Pananghat’s lab at the Indian Institute of Science Education and Research Pune (IISER Pune), and their research team emphasise the role of understanding protein structures for developing antibiotics. They uncover subtle differences that alter the drug activity of PC190723.
PC190723 is a benzamide, a small molecule that stops bacterial cells from dividing by targeting the key protein, FtsZ (Filamenting temperature-sensitive mutant Z). FtsZ is an important protein, similar to tubulin, and without it, cells cannot form the Z‑ring structure required for division, leading to cell death. This drug has been shown to effectively kill many types of harmful bacteria, including strains that are resistant to other antibiotics, such as MRSA (methicillin-resistant Staphylococcus aureus). However, it doesn’t work against the Gram-negative class of bacteria like Escherichia coli.
This limitation prompted Srinivasan and his graduate student, Sakshi Poddar, to investigate further.
Although Gram-negative bacteria also possess the FtsZ protein for cell division, there are subtle intra-molecular interactions within its structure that are different from that of Gram-positive bacteria, making Gram-negative bacteria more resistant to the drug. Chakraborty investigated these structural changes and deduced that intra-molecular interactions, as speculated by others, played a role. To stabilise their protein structures, amino acids sometimes form salt bridges—electrostatic interaction between two oppositely charged amino acids.
This meant that in Gram-negative bacteria, FtsZ contained additional chemical bonds in the form of these salt bridges, located near the drug’s binding site. As a result, the drug could no longer bind effectively to the protein, allowing these bacteria to survive. To confirm that the salt bridge was responsible for the resistance, Poddar used genetic techniques to introduce mutations in the gene, altering the amino acids responsible for the salt bridge formation. These single mutations were sufficient to render the bacterial cells sensitive to the drug.
Bacterial cells develop resistance to antibiotics at a much faster rate than other organisms. Unlike higher organisms, bacteria exchange DNA from one bacteria to another through a process called horizontal gene transfer.
One of the major factors driving this resistance is the overuse and misuse of antibiotics. Therefore, careful antibiotic design plays an essential role in overcoming antibiotic resistance.
Nishad Matange, Assistant Professor, IISER Pune, who is not part of the study says, “In my opinion, attempting to look for a single or foremost cause is futile. It is as much a problem within the realm of biology and medicine, as public health and economics. Thus, studies showcasing wider approaches to solving the problem is a key to future research.”
Srinivasan rightly points out that their study sheds light on the structural features of FtsZ that must be considered when designing new antibiotics targeting specific binding sites. With this new insight into drug designing for antibiotics targeting cell division, he believes they have opened new avenues for pharmaceutical companies to explore, testing new derivatives with minimal resistance. He adds, “I am hopeful that at least one derivative of PC190723 will eventually prove to be an effective antibiotic”.
The study highlights the significant importance of differences in intra-molecular interactions within similar protein structures in drug design. Matange exemplifies the brilliant capture of the nuanced differences between the protein structures and their effect on the anti-bacterial studied by the authors.